Hi James,

I'm not sure what I was thinking a year ago when I said dome projection would be difficult to add to ChimeraX.

http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-April/000471.html

It actually looks pretty easy because I long ago added to ChimeraX an equirectangular projection mode for making 360 videos. That mode is called 360 in the ChimeraX camera command.

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/camera.html https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/camera.html

Our docs need some more description, the equirectangular projection just means longitude 0-360 along x axis and lattitude -90 to 90 degrees on the y axis of the rectangle image. This is rendered from a cube map texture so the quality is good in all directions. To get a fish eye projection would just involve replacing a bit of code that defines how to map the cube map to a hemisphere.

I made a few planetarium biology videos long ago, one on HIV RNA,

https://www.youtube.com/watch?v=i-__ufO9LYg&t=15s https://www.youtube.com/watch?v=i-__ufO9LYg&t=15s

and another zooming in on the human brain to molecular scale

https://www.youtube.com/watch?v=RE2XMzInX_o

Those YouTube videos don't have the full fisheye hemisphere but I have those somewhere at 4k by 4k pixels if you are interested.

Tom

On Jan 16, 2020, at 11:25 AM, Tom Goddard goddard@sonic.net wrote:

Hi James,

Great to hear that Chimera dome projection has been useful. I'll look at how hard it would be to do it in ChimeraX. I am a fan of putting these unique features in if others will make beautiful presentations with it.

Tom

...

On Jan 15, 2020, at 6:31 AM, James Hedberg <jhedberg@ccny.cuny.edu mailto:jhedberg@ccny.cuny.edu> wrote:

Hi,

I see from previous threads (3/2019) that there are no plans to add the dome projection/fisheye mode for the camera control on ChimeraX:

"It would take some days of work to add dome camera mode to ChimeraX. We have no funding for that and very few people will use it so I'm afraid that is not likely to be implemented.”

I understand there is probably not a lot of current demand for this feature, however, in the spirit of Field of Dreams - if you build it, they will come. There is a growing interest in using planetariums/full domes for non-astro related sci-viz, yet very few tools available to do so. We’re currently using Chimera (regular) to do sci-viz in the planetarium for proteins and more. Knowing that this would be supported down the road when ChimeraX takes over (not sure when that will happen) would certainly be nice. You could make ChimeraX uniquely positioned to fill this deficit.

Anyway, just a hand raised here for an informal poll of ‘who wants dome mode’.

Thanks,

James

Dr. James Hedberg Physics Lecturer Director, CCNY Planetarium https://ccnyplanetarium.org/ City College of New York Department of Physics

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Hi James,

I added dome camera mode to ChimeraX (command "camera dome"). You probably want to show ChimeraX graphics full-screen to render it interactively on the dome with control panels on a separate screen, so I added a few commands to hide the extra ChimeraX window panes "ui statusbar false", "ui menubar false" (on windows), "ui fullscreen true" (this gets rid of the window titlebar). Also you can undock the command-line and toolbar (right click in those panels and uncheck Dockable Tool in the popup menu). All the other tools can be dragged out of the main window or closed, or you can hide them all with the icon in the lower right corner of the ChimeraX main window. I tried this on Mac and Windows but not Linux. The cube map used by ChimeraX uses 1024 x 1024 pixels per cube face. For higher resolution rendering you can increase that with for example "camera dome cubePixels 2048".

This stuff will be in tonight's ChimeraX daily builds if the succeed -- the builds have been broken for a few days due to various problems, so not sure if they will work tonight.

Tom

Image shows full screen graphics with toolbar and command-line undocked showing mouse brain electron microscopy with dome camera mode.

On Jan 17, 2020, at 7:29 AM, James Hedberg jhedberg@ccny.cuny.edu wrote:

Hi Tom,

Fantastic! Agreed - if you’re already making a cube map, then transforming to fisheye shouldn’t be terribly involved - that’s how our universe simulator currently does it. https://www.openspaceproject.com/ https://www.openspaceproject.com/

I did find your brain video some time ago when I was looking for things to show some admins in the hopes of sparking some more interests in our dome. It was great and inspired me to look more into this.

My long term goal is to be able to use the planetarium to fly (in real time) around the micro/nano-cosmos in the same we can fly around the galaxy and the universe. Possibly make some pre-rendered movies, but I enjoy the live shows better. I think Chimera(X) can possibly be part of that. More immediately, I’d like to use it to enable bio/med researchers to give science talks in the dome with full immersive visualizations. That’s the short term goal. I’m sure Chimera (regular) will be able to handle this in the mean time, but the improved capabilities and graphics of X will be nice to have in the future.

Thanks for investigating this functionality,

James

...

On Jan 16, 2020, at 9:45 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:

Hi James,

I'm not sure what I was thinking a year ago when I said dome projection would be difficult to add to ChimeraX.

http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-April/000471.html https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_pipermail_chimerax-2Dusers_2019-2DApril_000471.html&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=hNAbdO04_mEP-HQ1M6SKNVeeU-8bD646SphpdO6gpzs&m=n7gJN9c6JQz3P2a-1dV7GO9gRhWq-jyV8c-lV-dVhaw&s=OtG7o0aXzZXbq3x8xXzcKNQh4oaHHXttFTr7MjXu7JQ&e=

It actually looks pretty easy because I long ago added to ChimeraX an equirectangular projection mode for making 360 videos. That mode is called 360 in the ChimeraX camera command.

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/camera.html https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimerax_docs_user_commands_camera.html&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=hNAbdO04_mEP-HQ1M6SKNVeeU-8bD646SphpdO6gpzs&m=n7gJN9c6JQz3P2a-1dV7GO9gRhWq-jyV8c-lV-dVhaw&s=Oz__CCjpEhHNWwoHTapjLDRtCQuBrk6o2xgulPYw5I4&e=

Our docs need some more description, the equirectangular projection just means longitude 0-360 along x axis and lattitude -90 to 90 degrees on the y axis of the rectangle image. This is rendered from a cube map texture so the quality is good in all directions. To get a fish eye projection would just involve replacing a bit of code that defines how to map the cube map to a hemisphere.

I made a few planetarium biology videos long ago, one on HIV RNA,

https://www.youtube.com/watch?v=i-__ufO9LYg&t=15s https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_watch-3Fv-3Di-2D-5F-5FufO9LYg-26t-3D15s&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=hNAbdO04_mEP-HQ1M6SKNVeeU-8bD646SphpdO6gpzs&m=n7gJN9c6JQz3P2a-1dV7GO9gRhWq-jyV8c-lV-dVhaw&s=w0qALu8D84Oyoi4jqzzKgDtdqzYBHTg-LAnWcJoNZM0&e=

and another zooming in on the human brain to molecular scale

https://www.youtube.com/watch?v=RE2XMzInX_o https://www.youtube.com/watch?v=RE2XMzInX_o

Those YouTube videos don't have the full fisheye hemisphere but I have those somewhere at 4k by 4k pixels if you are interested.

Tom

...

On Jan 16, 2020, at 11:25 AM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:

Hi James,

Great to hear that Chimera dome projection has been useful. I'll look at how hard it would be to do it in ChimeraX. I am a fan of putting these unique features in if others will make beautiful presentations with it.

Tom

...

On Jan 15, 2020, at 6:31 AM, James Hedberg <jhedberg@ccny.cuny.edu mailto:jhedberg@ccny.cuny.edu> wrote:

Hi,

I see from previous threads (3/2019) that there are no plans to add the dome projection/fisheye mode for the camera control on ChimeraX:

"It would take some days of work to add dome camera mode to ChimeraX. We have no funding for that and very few people will use it so I'm afraid that is not likely to be implemented.”

I understand there is probably not a lot of current demand for this feature, however, in the spirit of Field of Dreams - if you build it, they will come. There is a growing interest in using planetariums/full domes for non-astro related sci-viz, yet very few tools available to do so. We’re currently using Chimera (regular) to do sci-viz in the planetarium for proteins and more. Knowing that this would be supported down the road when ChimeraX takes over (not sure when that will happen) would certainly be nice. You could make ChimeraX uniquely positioned to fill this deficit.

Anyway, just a hand raised here for an informal poll of ‘who wants dome mode’.

Thanks,

James

Dr. James Hedberg Physics Lecturer Director, CCNY Planetarium https://urldefense.proofpoint.com/v2/url?u=https-3A__ccnyplanetarium.org_&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=hNAbdO04_mEP-HQ1M6SKNVeeU-8bD646SphpdO6gpzs&m=n7gJN9c6JQz3P2a-1dV7GO9gRhWq-jyV8c-lV-dVhaw&s=2LHYB4Xm3Q7h_wc_kb8DS4bxHyRJuVn9LeRKG5Ia2sY&e= City College of New York Department of Physics

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Hi James,

Thanks for trying ChimeraX dome camera projection and sending the photo. Here are a few more thoughts.

I think using the dome live instead of with prerecorded video is the way to go. But the fisheye projection (image radius proportional to angle from pole) is probably not the right projection to get a distortion free image on the dome. If the hardware has a projector shining on a spherical mirror then some different projection would be better. This could pretty easily be changed in the ChimeraX code. The code that maps the projector image to directions on the sphere is just a few lines in ChimeraX Python file

ChimeraX.app/Contents/lib/python3.7/site-packages/chimerax/core/graphics/camera360.py

https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/core/graphics/camera360.... https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/core/graphics/camera360.py

In the DomeCamera projection_direction() method and you could just change that code and restart ChimeraX to warp in a different way. One way to see how much distortion you are getting would be to take a virus capsid from EMDB, show only half of it (volume command region option), position the view in dome mode so camera is centered at the virus center looking at the inside of the capsid icosahedron. Then see if it visually looks undistorted on the dome.

For using ChimeraX with the dome interactively I guess it will be hard to move slowly enough to avoid making viewers sick. The "view" command can move from one saved view point to another very slowly. But probably some other tools are needed to handle nice slow motions interactively.

Long ago I tried using Chimera for stereoscopic planetarium dome projection (I tried flying through the influenza M2 ion channel) in the Hilo Hawaii planetarium. ChimeraX can do stereoscopic 360 so it could probably be made to do it on the dome if you are interested. Here is a 360 stereo video example with ChimeraX.

https://www.rbvi.ucsf.edu/chimerax/docs/user/vrphone.html https://www.rbvi.ucsf.edu/chimerax/docs/user/vrphone.html

Of course requires a stereo capable projection (>= 120Hz refresh), and graphics card that can do stereo (e.g. Nvidia Quadro, not available on Mac), and stereo glasses (e.g. LCD plus IR emitter).

Tom

On Jan 24, 2020, at 6:35 AM, James Hedberg jhedberg@ccny.cuny.edu wrote:

Fantastic - I got it up and running and it looks and runs great! Thank you!

Next up: convince more folks to come down to the dome and play with it!

James

<IMG_8533.jpeg>

...

On Jan 21, 2020, at 10:35 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:

Hi James,

I added dome camera mode to ChimeraX (command "camera dome"). You probably want to show ChimeraX graphics full-screen to render it interactively on the dome with control panels on a separate screen, so I added a few commands to hide the extra ChimeraX window panes "ui statusbar false", "ui menubar false" (on windows), "ui fullscreen true" (this gets rid of the window titlebar). Also you can undock the command-line and toolbar (right click in those panels and uncheck Dockable Tool in the popup menu). All the other tools can be dragged out of the main window or closed, or you can hide them all with the icon in the lower right corner of the ChimeraX main window. I tried this on Mac and Windows but not Linux. The cube map used by ChimeraX uses 1024 x 1024 pixels per cube face. For higher resolution rendering you can increase that with for example "camera dome cubePixels 2048".

This stuff will be in tonight's ChimeraX daily builds if the succeed -- the builds have been broken for a few days due to various problems, so not sure if they will work tonight.

Tom

Image shows full screen graphics with toolbar and command-line undocked showing mouse brain electron microscopy with dome camera mode.

<dome_fullscreen.jpg>

...

On Jan 17, 2020, at 7:29 AM, James Hedberg <jhedberg@ccny.cuny.edu mailto:jhedberg@ccny.cuny.edu> wrote:

Hi Tom,

Fantastic! Agreed - if you’re already making a cube map, then transforming to fisheye shouldn’t be terribly involved - that’s how our universe simulator currently does it. https://www.openspaceproject.com/ https://urldefense.proofpoint.com/v2/url?u=https-3A__www.openspaceproject.com_&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=hNAbdO04_mEP-HQ1M6SKNVeeU-8bD646SphpdO6gpzs&m=YZUIF1xOCg9mP4w7ZhRnZAVAEw5qtu4NNnZ85PfsVe4&s=D8lBq6xu35S-6r_l0idQJXYAvdyg_vwJbM7rWS9GaGU&e=

I did find your brain video some time ago when I was looking for things to show some admins in the hopes of sparking some more interests in our dome. It was great and inspired me to look more into this.

My long term goal is to be able to use the planetarium to fly (in real time) around the micro/nano-cosmos in the same we can fly around the galaxy and the universe. Possibly make some pre-rendered movies, but I enjoy the live shows better. I think Chimera(X) can possibly be part of that. More immediately, I’d like to use it to enable bio/med researchers to give science talks in the dome with full immersive visualizations. That’s the short term goal. I’m sure Chimera (regular) will be able to handle this in the mean time, but the improved capabilities and graphics of X will be nice to have in the future.

Thanks for investigating this functionality,

James

...

On Jan 16, 2020, at 9:45 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:

Hi James,

I'm not sure what I was thinking a year ago when I said dome projection would be difficult to add to ChimeraX.

http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-April/000471.html https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_pipermail_chimerax-2Dusers_2019-2DApril_000471.html&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=hNAbdO04_mEP-HQ1M6SKNVeeU-8bD646SphpdO6gpzs&m=n7gJN9c6JQz3P2a-1dV7GO9gRhWq-jyV8c-lV-dVhaw&s=OtG7o0aXzZXbq3x8xXzcKNQh4oaHHXttFTr7MjXu7JQ&e=

It actually looks pretty easy because I long ago added to ChimeraX an equirectangular projection mode for making 360 videos. That mode is called 360 in the ChimeraX camera command.

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/camera.html https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimerax_docs_user_commands_camera.html&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=hNAbdO04_mEP-HQ1M6SKNVeeU-8bD646SphpdO6gpzs&m=n7gJN9c6JQz3P2a-1dV7GO9gRhWq-jyV8c-lV-dVhaw&s=Oz__CCjpEhHNWwoHTapjLDRtCQuBrk6o2xgulPYw5I4&e=

Our docs need some more description, the equirectangular projection just means longitude 0-360 along x axis and lattitude -90 to 90 degrees on the y axis of the rectangle image. This is rendered from a cube map texture so the quality is good in all directions. To get a fish eye projection would just involve replacing a bit of code that defines how to map the cube map to a hemisphere.

I made a few planetarium biology videos long ago, one on HIV RNA,

https://www.youtube.com/watch?v=i-__ufO9LYg&t=15s https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_watch-3Fv-3Di-2D-5F-5FufO9LYg-26t-3D15s&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=hNAbdO04_mEP-HQ1M6SKNVeeU-8bD646SphpdO6gpzs&m=n7gJN9c6JQz3P2a-1dV7GO9gRhWq-jyV8c-lV-dVhaw&s=w0qALu8D84Oyoi4jqzzKgDtdqzYBHTg-LAnWcJoNZM0&e=

and another zooming in on the human brain to molecular scale

https://www.youtube.com/watch?v=RE2XMzInX_o https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_watch-3Fv-3DRE2XMzInX-5Fo&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=hNAbdO04_mEP-HQ1M6SKNVeeU-8bD646SphpdO6gpzs&m=YZUIF1xOCg9mP4w7ZhRnZAVAEw5qtu4NNnZ85PfsVe4&s=DiFzodbLuMs7pY2_O7u4pXxq7k4oT-VcZ2n4ndimQio&e=

Those YouTube videos don't have the full fisheye hemisphere but I have those somewhere at 4k by 4k pixels if you are interested.

Tom

...

On Jan 16, 2020, at 11:25 AM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:

Hi James,

Great to hear that Chimera dome projection has been useful. I'll look at how hard it would be to do it in ChimeraX. I am a fan of putting these unique features in if others will make beautiful presentations with it.

Tom

...

On Jan 15, 2020, at 6:31 AM, James Hedberg <jhedberg@ccny.cuny.edu mailto:jhedberg@ccny.cuny.edu> wrote:

Hi,

I see from previous threads (3/2019) that there are no plans to add the dome projection/fisheye mode for the camera control on ChimeraX:

"It would take some days of work to add dome camera mode to ChimeraX. We have no funding for that and very few people will use it so I'm afraid that is not likely to be implemented.”

I understand there is probably not a lot of current demand for this feature, however, in the spirit of Field of Dreams - if you build it, they will come. There is a growing interest in using planetariums/full domes for non-astro related sci-viz, yet very few tools available to do so. We’re currently using Chimera (regular) to do sci-viz in the planetarium for proteins and more. Knowing that this would be supported down the road when ChimeraX takes over (not sure when that will happen) would certainly be nice. You could make ChimeraX uniquely positioned to fill this deficit.

Anyway, just a hand raised here for an informal poll of ‘who wants dome mode’.

Thanks,

James

Dr. James Hedberg Physics Lecturer Director, CCNY Planetarium https://urldefense.proofpoint.com/v2/url?u=https-3A__ccnyplanetarium.org_&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=hNAbdO04_mEP-HQ1M6SKNVeeU-8bD646SphpdO6gpzs&m=n7gJN9c6JQz3P2a-1dV7GO9gRhWq-jyV8c-lV-dVhaw&s=2LHYB4Xm3Q7h_wc_kb8DS4bxHyRJuVn9LeRKG5Ia2sY&e= City College of New York Department of Physics

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